arXiv subjects

Shi Huang

Publications and source records attributed to Shi Huang.

10 recordsLinked to original sources

arXiv2025

Operando study of the evolution of peritectic structures in metal solidification by quasi-simultaneous synchrotron X-ray diffraction and tomography

Using quasi-simultaneous synchrotron X-ray diffraction and tomography techniques, we have studied in-situ and in real-time the nucleation and co-growth dynamics of the peritectic structures in an Al-Mn alloy during solidification. We collected ~30 TB 4D datasets which allow us to elucidate the phases' co-growth dynamics and their spatial, crystallographic and compositional relationship. The primary Al4Mn hexagonal prisms nucleate and grow with high kinetic anisotropy -70 times faster in the axial direction than the radial direction. In all cases, a ~5 um Mn-rich diffusion layer forms at the liquid-solid interface, creating a sharp local solute gradient that governs subsequent phase transformation. The peritectic Al6Mn phases nucleate epitaxially within this diffusion zone, initially forming a thin shell surrounding the Al4Mn with an orientation relationship of {10-10}HCP // {110}O, [0001]HCP // [001]O. Such ~5 um Mn-rich diffusion layers also cause solute depletion at the liquid side of the liquid-solid interface, limiting further epitaxial phase growth, but prompting phase re-nucleation and branching at crystal edges, resulting tetragonal prism structures that no longer follow the initial orientation relationship. The anisotropic diffusion also led to the formation of core defects at the centre of both phases. Furthermore, increasing cooling rate from 0.17 to 20 {\deg}C/s can disrupt the stability of the solute diffusion zone, effectively suppressing the formation of the core defects and forcing a transition from faceted to non-faceted morphologies. Our work establishes a new theoretical framework for how to tailor and control the peritectic structures in metallic alloys through solidification processes.

cond-mat.mtrl-sci↗

arXiv2023

Ultrasound cavitation and exfoliation dynamics of 2D materials re-vealed in operando by X-ray free electron laser megahertz imaging

Ultrasonic liquid phase exfoliation is a promising method for the production of two-dimensional (2D) layered materials. A large number of studies have been made in investigating the underlying ultrasound exfoliation mechanisms. However, due to the experimental challenges for capturing the highly transient and dynamic phenomena in real-time at sub-microsecond time and micrometer length scales simultaneously, most theories reported to date still remain elusive. Here, using the ultra-short X-ray Free Electron Laser pulses (~25ps) with a unique pulse train structure, we applied MHz X-ray Microscopy and machine-learning technique to reveal unambiguously the full cycles of the ultrasound cavitation and graphite layer exfoliation dynamics with sub-microsecond and micrometer resolution. Cyclic fatigue shock wave impacts produced by ultrasound cloud implosion were identified as the dominant mechanism to deflect and exfoliate graphite layers mechanically. For the graphite flakes, exfoliation rate as high as ~5 angstroms per shock wave impact was observed. For the HOPG graphite, the highest exfoliation rate was ~0.15 angstroms per impact. These new findings are scientifically and technologically important for developing industrial upscaling strategies for ultrasonic exfoliation of 2D materials.

cond-mat.mtrl-sci↗

arXiv2022

3D Path Planning and Obstacle Avoidance Algorithms for Obstacle-Overcoming Robots

This article introduces a multimodal motion planning (MMP) algorithm that combines three-dimensional (3-D) path planning and a DWA obstacle avoidance algorithm. The algorithms aim to plan the path and motion of obstacle-overcoming robots in complex unstructured scenes. A novel A-star algorithm is proposed to combine the characteristics of unstructured scenes and a strategy to switch it into a greedy best-first strategy algorithm. Meanwhile, the algorithm of path planning is integrated with the DWA algorithm so that the robot can perform local dynamic obstacle avoidance during the movement along the global planned path. Furthermore, when the proposed global path planning algorithm combines with the local obstacle avoidance algorithm, the robot can correct the path after obstacle avoidance and obstacle overcoming. The simulation experiments in a factory with several complex environments verified the feasibility and robustness of the algorithms. The algorithms can quickly generate a reasonable 3-D path for obstacle-overcoming robots and perform reliable local obstacle avoidance under the premise of considering the characteristics of the scene and motion obstacles.

cs.RO↗

arXiv2020

Utilizing stability criteria in choosing feature selection methods yields reproducible results in microbiome data

Feature selection is indispensable in microbiome data analysis, but it can be particularly challenging as microbiome data sets are high-dimensional, underdetermined, sparse and compositional. Great efforts have recently been made on developing new methods for feature selection that handle the above data characteristics, but almost all methods were evaluated based on performance of model predictions. However, little attention has been paid to address a fundamental question: how appropriate are those evaluation criteria? Most feature selection methods often control the model fit, but the ability to identify meaningful subsets of features cannot be evaluated simply based on the prediction accuracy. If tiny changes to the training data would lead to large changes in the chosen feature subset, then many of the biological features that an algorithm has found are likely to be a data artifact rather than real biological signal. This crucial need of identifying relevant and reproducible features motivated the reproducibility evaluation criterion such as Stability, which quantifies how robust a method is to perturbations in the data. In our paper, we compare the performance of popular model prediction metric MSE and proposed reproducibility criterion Stability in evaluating four widely used feature selection methods in both simulations and experimental microbiome applications. We conclude that Stability is a preferred feature selection criterion over MSE because it better quantifies the reproducibility of the feature selection method.

q-bio.QM↗

arXiv2020

Modern alleles in archaic human Y chromosomes support origin of modern human paternal lineages in Asia rather than Africa

Recent studies have shown that hybridization between modern and archaic humans was commonplace in the history of our species. After admixture, some individuals with admixed autosomes carried the modern Homo Sapiens uniparental DNAs, while the rest carried the archaic versions. Coevolution of admixed autosomes and uniparental DNAs is expected to cause some of the sites in modern uniparental DNAs to revert back to archaic alleles, while the opposite process would occur (from archaic to modern) in some of the sites in archaic uniparental DNAs. This type of coevolution is one of the elements that differentiate the two different models of the Y phylogenetic tree of modern humans, rooting it either in Africa or East Asia. The expected reversion to archaic alleles is assumed to occur and is easily traceable in the Asia model, but is absent in the Africa model due to its infinite site assumption, which also precludes the independent or convergent mutation to modern alleles in archaic uniparental DNAs since mutations are assumed to occur randomly across a neutral genome, and convergent evolution is assumed not to occur. Here, we examined newly published high coverage Y chromosome sequencing data of two Denisovan and two Neanderthal samples to determine whether they carry modern-Homo Sapiens alleles in sites where they are not supposed to according to the Africa model. The results showed that a significant fraction of the sites that, according to the Asia model, should differentiate the original modern Y from the original archaic Y carried modern alleles in the archaic Y samples here. Some of these modern alleles were shared among all archaic humans while others could differentiate Denisovans from Neanderthals. The observation is best accounted for by coevolution of archaic Y and admixed modern autosomes, and hence supports the Asia model, since it takes such coevolution into account.

q-bio.OT↗

arXiv2018

Surpassing the Ambient Packing Limit of Energetic Crystals: Squeezing Effect of Molecular Level "Net-fishing"

High energy density is always a key goal for developments of energy storage or energetic materials (EMs). Except exploring novel EMs with high chemical energy, it is also desirable if the traditional EMs could be assembled at a higher density. However, it is very difficult to surpass their theoretical maximum molecular packing density under ambient conditions, even though a higher density could be achieved under ultra-high pressure (Gigapascals). Such solid-state phase changes are reversible, and hence this high density packing is not able to maintain under ambient conditions. Alternatively, in this research, we demonstrated a molecular level compression effect by stacking of 2-D TAGP, resulting in a higher density packing of the HMX molecules with changed conformation. The HMX crystal formed under compression in the solvent has a unit cell parameter very close to the reported one observed under pressure of 0.2 GPa. It shows that the compressed HMX molecules are trapped in the TAGP layers, resulting in a higher density (e.g. 2.13 g cm-3) and also higher heat of formation. The resulted HMX crystals are free of defects, and unlike the pristine HMX, no polymorphic transition and melting point were observed upon heating. Experiments and relevant calculations show that the best resulted hybrid HMX crystal has a detonation velocity of 10.40 km s-1 and pressure of 53.9 GPa, respectively. Its ground specific impulse reaches about 292 s, even much better than CL-20, making it a promising propellant component for future space explorations.

cond-mat.mtrl-sci↗

arXiv2015

New thoughts on an old riddle: what determines genetic diversity within and between species?

The question of what determines genetic diversity both between and within species has long remained unsolved by the modern evolutionary theory (MET). However, it has not deterred researchers from producing interpretations of genetic diversity by using MET. We here examine the two key experimental observations of genetic diversity made in the 1960s, one between species and the other within a population of a species, that directly contributed to the development of MET. The interpretations of these observations as well as the assumptions by MET are widely known to be inadequate. We review the recent progress of an alternative framework, the maximum genetic diversity (MGD) hypothesis, that uses axioms and natural selection to explain the vast majority of genetic diversity as being at optimum equilibrium that is largely determined by organismal complexity. The MGD hypothesis fully absorbs the proven virtues of MET and considers its assumptions relevant only to a much more limited scope. This new synthesis has accounted for the much overlooked phenomenon of progression towards higher complexity, and more importantly, been instrumental in directing productive research into both evolutionary and biomedical problems.

q-bio.PE↗

arXiv2013

Methods for scoring the collective effect of SNPs: Minor alleles of common SNPs quantitatively affect traits/diseases and are under both positive and negative selection

Most common SNPs are popularly assumed to be neutral. We here developed novel methods to examine in animal models and humans whether extreme amount of minor alleles (MAs) carried by an individual may represent extreme trait values and common diseases. We analyzed panels of genetic reference populations and identified the MAs in each panel and the MA content (MAC) that each strain carried. We also analyzed 21 published GWAS datasets of human diseases and identified the MAC of each case or control. MAC was nearly linearly linked to quantitative variations in numerous traits in model organisms, including life span, tumor susceptibility, learning and memory, sensitivity to alcohol and anti-psychotic drugs, and two correlated traits poor reproductive fitness and strong immunity. Similarly, in Europeans or European Americans, enrichment of MAs of fast but not slow evolutionary rate was linked to autoimmune and numerous other diseases, including type 2 diabetes, Parkinson's disease, psychiatric disorders, alcohol and cocaine addictions, cancer, and less life span. Therefore, both high and low MAC correlated with extreme values in many traits, indicating stabilizing selection on most MAs. The methods here are broadly applicable and may help solve the missing heritability problem in complex traits and diseases.

q-bio.GN↗

arXiv2013

Role of genetic polymorphisms in transgenerational inheritance in budding yeast

Transgenerational inheritance of a trait is presumably affected by both genetic and environmental factors but remains poorly understood. We studied the effect of genetic polymorphisms on transgenerational inheritance of yeast segregants that were derived from a cross between a laboratory strain and a wild strain of Saccharomyces cerevisiae. For each SNP analyzed, the parental allele present in less than half of the segregants panel was called the minor allele (MA). We found a nonrandom distribution of MAs in the segregants, indicating natural selection. We compared segregants with high MA content (MAC) relative to those with less and found a more dramatic shortening of the lag phase length for the high MAC group in response to 14 days of ethanol training. Also, the short lag phase as acquired and epigenetically memorized by ethanol training was more dramatically lost after 7 days of recovery in ethanol free medium for the high MAC group. Sodium chloride treatment produced similar observations. Using public datasets, we found MAC linkage to mRNA expression of hundreds of genes. Finally, we found preferential effect of MAC on traits with high number of known additive quantitative trait loci (QTLs). These results provide evidence for the slightly deleterious nature of most MAs and a lower capacity to maintain inheritance of traits in individuals or cells with greater MAC, which have implications for disease prevention and treatment and the "missing heritability" problem in complex traits and diseases.

q-bio.GN↗

arXiv2008

Modeling the creative process of the mind by prime numbers and a simple proof of the Riemann Hypothesis

Numbers (positive integers) are the most fundamental creatures of the human mind and the foundation to the scientific understanding of nature. Some mathematicians have suspected a link between prime numbers and secrets of creation. Understanding creativity may help resolve the deepest mysteries of primes. The algorithm that programs the mind and makes the mind creative must be sufficient for the mind to create primes. I found that primes are directly linked to the creation algorithm of the mind. The essence of primes is the duality of uniqueness and uniformity together with the creation algorithm of the mind. The creative process of the mind is lawfully determined but the outcome is unpredictable. The mathematical equivalent or model of this process is the creation of primes. Primes have the inherent property of unpredictability but can be generated by the creation algorithm of the mind, termed the Prime Law, via a fully deterministic lawful process. This new understanding of the essence of primes can deduce some of the best-known properties of primes, including the Riemann Hypothesis (RH). Understanding human creativity is obviously the most fundamental of all scientific enquiries. That this understanding can directly lead to a solution to the RH, widely considered the most important unsolved problem in mathematics, shows a deep connection between creativity and mathematics.

math.GM↗